IQ-TREE
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model-finder -madd option ignored in version 2
Model-Finder appears to ignore model codes input via the -madd option when using IQ-TREE version 2.0.3 (installed via Conda) and 2.1.1 (for MacOS). However, it works as expected when I use IQ-TREE version 1.6.12.
This is the command that I ran, which ignores the -madd option with version 2:
iqtree -s alignment.afaa -m MF -madd C20